-Clazz.declarePackage ("jalview.appletgui");\r
-Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.historyList = null;\r
-this.redundancy = null;\r
-this.originalSequences = null;\r
-this.frame = null;\r
-this.redundantSeqs = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]);\r
-Clazz.prepareFields (c$, function () {\r
-this.historyList = new java.util.Stack ();\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (ap) {\r
-Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]);\r
-this.redundantSeqs = new java.util.Vector ();\r
-this.ap = ap;\r
-this.undoButton.setVisible (true);\r
-this.applyButton.setVisible (true);\r
-this.allGroupsCheck.setVisible (false);\r
-this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));\r
-this.valueField.setText ("100");\r
-this.slider.setVisibleAmount (1);\r
-this.slider.setMinimum (0);\r
-this.slider.setMaximum (100 + this.slider.getVisibleAmount ());\r
-this.slider.setValue (100);\r
-this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null)));\r
-this.frame = new awt2swing.Frame ();\r
-this.frame.add (this);\r
-jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100);\r
-this.frame.addWindowListener (this);\r
-var worker = new Thread (this);\r
-worker.start ();\r
-}, "jalview.appletgui.AlignmentPanel");\r
-Clazz.overrideMethod (c$, "run", \r
-function () {\r
-this.label.setText (jalview.util.MessageManager.getString ("label.calculating"));\r
-this.slider.setVisible (false);\r
-this.applyButton.setEnabled (false);\r
-this.valueField.setVisible (false);\r
-this.validate ();\r
-var omitHidden = null;\r
-var sg = this.ap.av.getSelectionGroup ();\r
-var height;\r
-var start;\r
-var end;\r
-if ((sg != null) && (sg.getSize () >= 1)) {\r
-this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ());\r
-start = sg.getStartRes ();\r
-end = sg.getEndRes ();\r
-} else {\r
-this.originalSequences = this.ap.av.getAlignment ().getSequencesArray ();\r
-start = 0;\r
-end = this.ap.av.getAlignment ().getWidth ();\r
-}height = this.originalSequences.length;\r
-this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false);\r
-this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));\r
-this.slider.setVisible (true);\r
-this.applyButton.setEnabled (true);\r
-this.valueField.setVisible (true);\r
-this.validate ();\r
-this.sliderValueChanged ();\r
-});\r
-Clazz.defineMethod (c$, "sliderValueChanged", \r
-function () {\r
-if (this.redundancy == null) {\r
-return;\r
-}var value = this.slider.getValue ();\r
-var redundantSequences = new java.util.ArrayList ();\r
-for (var i = 0; i < this.redundancy.length; i++) {\r
-if (value <= this.redundancy[i]) {\r
-redundantSequences.add (this.originalSequences[i]);\r
-}}\r
-this.ap.idPanel.idCanvas.setHighlighted (redundantSequences);\r
-jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);\r
-});\r
-Clazz.overrideMethod (c$, "applyButton_actionPerformed", \r
-function () {\r
-var del = new java.util.Vector ();\r
-this.undoButton.setEnabled (true);\r
-var value = this.slider.getValue ();\r
-var sg = this.ap.av.getSelectionGroup ();\r
-for (var i = 0; i < this.redundancy.length; i++) {\r
-if (value <= this.redundancy[i]) {\r
-del.addElement (this.originalSequences[i]);\r
-}}\r
-if (del.size () > 0) {\r
-var deleted = new Array (del.size ());\r
-var width = 0;\r
-for (var i = 0; i < del.size (); i++) {\r
-deleted[i] = del.elementAt (i);\r
-if (deleted[i].getLength () > width) {\r
-width = deleted[i].getLength ();\r
-}}\r
-var cut = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ());\r
-var alignment = this.ap.av.getAlignment ();\r
-for (var i = 0; i < del.size (); i++) {\r
-alignment.deleteSequence (deleted[i]);\r
-if (sg != null) {\r
-sg.deleteSequence (deleted[i], false);\r
-}}\r
-this.historyList.push (cut);\r
-this.ap.alignFrame.addHistoryItem (cut);\r
-jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);\r
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());\r
-}});\r
-Clazz.overrideMethod (c$, "undoButton_actionPerformed", \r
-function () {\r
-var command = this.historyList.pop ();\r
-command.undoCommand (null);\r
-if (this.ap.av.getHistoryList ().contains (command)) {\r
-this.ap.av.getHistoryList ().remove (command);\r
-this.ap.alignFrame.updateEditMenuBar ();\r
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());\r
-}this.ap.paintAlignment (true);\r
-if (this.historyList.size () == 0) {\r
-this.undoButton.setEnabled (false);\r
-}});\r
-Clazz.defineMethod (c$, "valueField_actionPerformed", \r
-function (e) {\r
-try {\r
-var i = Integer.parseInt (this.valueField.getText ());\r
-this.slider.setValue (i);\r
-} catch (ex) {\r
-if (Clazz.exceptionOf (ex, Exception)) {\r
-this.valueField.setText (this.slider.getValue () + "");\r
-} else {\r
-throw ex;\r
-}\r
-}\r
-}, "java.awt.event.ActionEvent");\r
-Clazz.overrideMethod (c$, "windowOpened", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowClosing", \r
-function (evt) {\r
-this.ap.idPanel.idCanvas.setHighlighted (null);\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowClosed", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowActivated", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowDeactivated", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowIconified", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-Clazz.overrideMethod (c$, "windowDeiconified", \r
-function (evt) {\r
-}, "java.awt.event.WindowEvent");\r
-c$.$RedundancyPanel$1$ = function () {\r
-Clazz.pu$h(self.c$);\r
-c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener);\r
-Clazz.overrideMethod (c$, "adjustmentValueChanged", \r
-function (evt) {\r
-this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + "");\r
-this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged ();\r
-}, "java.awt.event.AdjustmentEvent");\r
-c$ = Clazz.p0p ();\r
-};\r
-});\r
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.historyList = null;
+this.redundancy = null;
+this.originalSequences = null;
+this.frame = null;
+this.redundantSeqs = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]);
+Clazz.prepareFields (c$, function () {
+this.historyList = new java.util.Stack ();
+});
+Clazz.makeConstructor (c$,
+function (ap) {
+Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]);
+this.redundantSeqs = new java.util.Vector ();
+this.ap = ap;
+this.undoButton.setVisible (true);
+this.applyButton.setVisible (true);
+this.allGroupsCheck.setVisible (false);
+this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
+this.valueField.setText ("100");
+this.slider.setVisibleAmount (1);
+this.slider.setMinimum (0);
+this.slider.setMaximum (100 + this.slider.getVisibleAmount ());
+this.slider.setValue (100);
+this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null)));
+this.frame = new awt2swing.Frame ();
+this.frame.add (this);
+jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100);
+this.frame.addWindowListener (this);
+var worker = new Thread (this);
+worker.start ();
+}, "jalview.appletgui.AlignmentPanel");
+Clazz.overrideMethod (c$, "run",
+function () {
+this.label.setText (jalview.util.MessageManager.getString ("label.calculating"));
+this.slider.setVisible (false);
+this.applyButton.setEnabled (false);
+this.valueField.setVisible (false);
+this.validate ();
+var omitHidden = null;
+var sg = this.ap.av.getSelectionGroup ();
+var height;
+var start;
+var end;
+if ((sg != null) && (sg.getSize () >= 1)) {
+this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ());
+start = sg.getStartRes ();
+end = sg.getEndRes ();
+} else {
+this.originalSequences = this.ap.av.getAlignment ().getSequencesArray ();
+start = 0;
+end = this.ap.av.getAlignment ().getWidth ();
+}height = this.originalSequences.length;
+this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false);
+this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
+this.slider.setVisible (true);
+this.applyButton.setEnabled (true);
+this.valueField.setVisible (true);
+this.validate ();
+this.sliderValueChanged ();
+});
+Clazz.defineMethod (c$, "sliderValueChanged",
+function () {
+if (this.redundancy == null) {
+return;
+}var value = this.slider.getValue ();
+var redundantSequences = new java.util.ArrayList ();
+for (var i = 0; i < this.redundancy.length; i++) {
+if (value <= this.redundancy[i]) {
+redundantSequences.add (this.originalSequences[i]);
+}}
+this.ap.idPanel.idCanvas.setHighlighted (redundantSequences);
+jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
+});
+Clazz.overrideMethod (c$, "applyButton_actionPerformed",
+function () {
+var del = new java.util.Vector ();
+this.undoButton.setEnabled (true);
+var value = this.slider.getValue ();
+var sg = this.ap.av.getSelectionGroup ();
+for (var i = 0; i < this.redundancy.length; i++) {
+if (value <= this.redundancy[i]) {
+del.addElement (this.originalSequences[i]);
+}}
+if (del.size () > 0) {
+var deleted = new Array (del.size ());
+var width = 0;
+for (var i = 0; i < del.size (); i++) {
+deleted[i] = del.elementAt (i);
+if (deleted[i].getLength () > width) {
+width = deleted[i].getLength ();
+}}
+var cut = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ());
+var alignment = this.ap.av.getAlignment ();
+for (var i = 0; i < del.size (); i++) {
+alignment.deleteSequence (deleted[i]);
+if (sg != null) {
+sg.deleteSequence (deleted[i], false);
+}}
+this.historyList.push (cut);
+this.ap.alignFrame.addHistoryItem (cut);
+jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}});
+Clazz.overrideMethod (c$, "undoButton_actionPerformed",
+function () {
+var command = this.historyList.pop ();
+command.undoCommand (null);
+if (this.ap.av.getHistoryList ().contains (command)) {
+this.ap.av.getHistoryList ().remove (command);
+this.ap.alignFrame.updateEditMenuBar ();
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}this.ap.paintAlignment (true);
+if (this.historyList.size () == 0) {
+this.undoButton.setEnabled (false);
+}});
+Clazz.defineMethod (c$, "valueField_actionPerformed",
+function (e) {
+try {
+var i = Integer.parseInt (this.valueField.getText ());
+this.slider.setValue (i);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+this.valueField.setText (this.slider.getValue () + "");
+} else {
+throw ex;
+}
+}
+}, "java.awt.event.ActionEvent");
+Clazz.overrideMethod (c$, "windowOpened",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowClosing",
+function (evt) {
+this.ap.idPanel.idCanvas.setHighlighted (null);
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowClosed",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowActivated",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowDeactivated",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowIconified",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowDeiconified",
+function (evt) {
+}, "java.awt.event.WindowEvent");
+c$.$RedundancyPanel$1$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener);
+Clazz.overrideMethod (c$, "adjustmentValueChanged",
+function (evt) {
+this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + "");
+this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged ();
+}, "java.awt.event.AdjustmentEvent");
+c$ = Clazz.p0p ();
+};
+});
git://source.jalview.org / jalviewjs.git / blobdiff